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The percentage identity between the reference copy and ORF1 ranges between 96% and 99%, meaning that these copies have not diverged much.
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For 6 families (Hopi/Osr27, Osr2, Osr8, Osr20, Osr34 and Osr44), the slight difference in size between the longest copy and the reference copy (99.3 to 99.9% of the reference copy size) is due to the homogenization of the two LTRs in the reference copy (see Material and Methods).
Length of the reference copy; Mean and standard error of the length between Helena copies; Mean and standard error (in parentheses) of percentage identity between Helena copies and the reference sequence Helena copies [ 18] Table 2 shows the average GC content for the upstream and downstream regions of the Helena insertions for each species.
First, we expected that the longest copy detected and the reference copy would have the same size because insertions in genomic copies (as compared to the reference copy) were not taken into account in the computation of the copy size.
To check for such possible insertions in the reference copies, we aligned all the mined genomic copies on their corresponding reference copies, and looked for subsets of copies that were a complete match with the same region of the reference copy.
In the other species in the melanogaster group, the reference copies are smaller than the Helena reference copy in D. simulans.
The TERT locus was used for the internal reference copy number.
To determine the copy number in each species, the previously-determined reference copy was blasted against the full genomes.
The reference single copy gene used in this study was human [beta] globin (hbg).
The reference single copy gene 36B4 was used as a loading control.
The TERT locus was used as an internal reference copy number.
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